extractSpliceSites {SPLINTER} | R Documentation

## extractSpliceSites

### Description

Extracts and formats to bed the location of target, upstream and downstream splice sites

### Usage

    extractSpliceSites(df, target = "SE", site = "donor",
      motif_range = c(-3, 6), start0 = TRUE)

### Arguments

`df` | extractSpliceEvents object
`target` | the target site to extract. See Details.
`site` | character donor or acceptor
`motif_range` | numeric vector of splice position to extract
`start0` | boolean 0-base start

### Details

target : the site to extract the sequence from. It can be either the event in question (SE, RI, MXE - first exon, MXE2 - second exon, A5SSlong, A5SSshort, A3SSlong, A3SSshort, upstream or downstream). If this function is used in conjunction with shapiroDonor or shapiroAcceptor to compute scores, then most likely it will be run twice - once for the event, and the other either up- or downstream as a comparison.

### Value

GRanges object

### Author(s)

Diana Low

### See Also

http://rnaseq-mats.sourceforge.net/user_guide.htm for MATS file definition

### Examples

    data_path<-system.file("extdata",package="SPLINTER")
    splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
    splice_sites<-extractSpliceSites(splice_data,target="SE")

[Package SPLINTER version 1.8.1 Index]